Effect of Genetic Response to Endophyte-Infected Fescue on Beef Cattle Gastrointestinal Tract Microbiota

Fescue toxicosis (FT) is a major disease in cattle, caused by consumption of endophyte-infected fescue. Although FT has great negative impact in the beef industry, little is known about genetic variation to FT, especially regarding its association with the gastrointestinal tract (GIT) microbiota. The objective of this study was to categorize and quantify the fecal microbiota of cows with contrasting response to FT. Weekly body weight (BW) data on 149 multiparous purebred pregnant, 2-4 yr old, Angus cows were collected for 13 weeks (April to July) at two locations in NC (Butner and Reidsville). Forty cows with contrasting performance were ranked and then classified as either high tolerant (HT) or low tolerant (LT) to FT. Animals were selected based on their average weekly gain (regression of BW on weeks) after adjustment for fixed-effects of parity, location, and initial body weight, with 20 cows in each group balanced by location. Fecal samples were collected at the end of the trial to capture variation during chronic exposure to the toxins. Samples were used for DNA extraction and 16S rRNA gene based Illumina MiSeq sequencing. Sequence analysis was done with mothur. After quality control, 58,400 reads remained per sample. Reads were clustered into Operational Taxonomic Units (OTU) with a 97% similarity cutoff. Statistical analyses revealed significant shifts in the composition of the microbial communities between the two tolerance groups, 146 OTUs were significantly more abundant (P<0.05) in the HT group, whereas 17 OTUs including OTUs related to Solibacillus, Bacillus, Psychrobacillus, Acinetobacter, and Arthrobacter were significantly (P<0.001) more abundant in LT cows, suggesting that these phylotypes may be linked to a more severe response to FT. Similarly, comparing the tolerance groups at the whole community level using non-metric multidimensional scaling (NMDS) and analysis of molecular variance (AMOVA) revealed significant (P<0.001) differences in composition between the GIT microbial communities of the two tolerance groups. Our results represent the first deep insights into changes in the GIT microbiome induced by feeding endophyte-infected fescue in cattle. Furthermore, our results reveal candidate bacteria which may be associated with host-genetic variation in response to fescue toxicosis.